Trypanosoma cruzi and Leishmania sp. are important protozoan parasites for humans and animals in the Americas, causing Chagas disease and cutaneous or visceral leishmaniasis, respectively. These vector-borne diseases affect permanent and transient populations in developing tropical countries that exhibit favorable conditions for the perpetuation of the parasite cycle. Our objective was to investigate the occurrence of infection with these parasites in wild animals from urban rainforest fragments in the city of Salvador, the largest city in the northeast region of Brazil. Sixty-five wild animals were captured, clinically examined, and sampled for parasite detection by PCR and culture. Ten different mammalian genera were identified, being 58% (38/65) marsupials. The prevalence of T. cruzi and Leishmania sp. infections was 13% and 43%, respectively. Both parasites were detected by PCR in 11% (7/65), three of which were also double infected as determined by culture. Among the 28 animals found infected with at least one parasite (43%, 28/65), 68% (19/28) were marsupials, two specimens were Callithrix sp. (7%), and one was Trinomys sp. (3%). Most infected animals (89%) had no clinical signs of disease. We found that healthy free-living animals from urban rainforest fragments harbored pathogenic trypanosomatids and should be included in epidemiology studies of diseases in big cities in tropical countries, as these cities grow and engulf rainforest remnants.